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I'd recommend to back up your entire Home folder (user account folder) if possible. So that, you can restore all the settings, files, documents etc back to your Mac after a clean install. Your home folder doesn't include the system files or applications. It just have the application settings, documents, preferences etc
If you only want to save the Safari history, then you have to backup the com.apple.safari.plist, history.plist files etc
Open Macintosh HD
, open Users
folder. Open your home folder. Open Library folder. Backup the entire Safari folder. The folder contains the history, bookmarks etc
Then open the Preferences folder and backup the file named com.apple.safari.plist
too. This is the configuration of your Safari application.
For applications (i.e 2 and 3), unfortunately you will have to reinstall them. You can't backup installed applications.
You can't also backup your Updates. You have to redownload them as well. You can download and install the 10.4.11 Combo Update from below links (download the correct one for your Mac);
Mac OS X 10.4.11 Combo Update for Intel : http://support.apple.com/kb/dl172
Mac OS X 10.4.11 Combo Update for PPC : http://support.apple.com/kb/dl170
If you've any questions or would like any additional information, please don't hesitate to ask.